Changes between Version 117 and Version 118 of Scripts


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Timestamp:
Jul 16, 2019, 10:41:54 AM (7 years ago)
Author:
meng
Comment:

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  • Scripts

    v117 v118  
    99These Python scripts provide capabilities not available using Chimera commands.  They may only work with specific Chimera versions.
    1010
     11 * [attachment:pruneCoordSets.py pruneCoordSets.py].  Prune away inactive coordinate sets to reduce session-file size.  Tested with Chimera 1.13.1 on April 28, 2019
    1112 * [attachment:mapdiff.py mapdiff.py]. Report maximum and minimum values of difference between two maps. Tested with Chimera 1.13.  September 6, 2018.
    1213 * [attachment:mean_distance.py mean_distance.py]. Compute ensemble atoms distance from mean. Tested with Chimera 1.12.  May 3, 2018.
    … …  
    1415 * [attachment:removecross.py removecross.py]. Remove longer pseudobonds that cross shorter pseudobonds. Tested with Chimera 1.11.2.  October 12, 2017.
    1516 * [attachment:segment.py segment.py]. Run segger to segment map. Tested with Chimera 1.11.2.  October 6, 2017.
     17 * [attachment:worm.py worm.py].  Create a "worms" depiction based on mavConservation attribute.  Script easily edited to use different attribute and different worm widths.  Tested with Chimera 1.11.2 on July 13, 2017.
    1618 * [attachment:dividelinks.py dividelinks.py]. Divide marker set links by inserting N additional markers. Tested with Chimera 1.11.2.  May 26, 2017.
    1719 * [attachment:save.py save.py]. Save a pdb fit to a map to files. Tested with Chimera 1.11.2.  April 20, 2017.
     20 * [attachment:radius-of-gyration-mass.py radius-of-gyration-mass.py].  Print center of mass and mass-weighted radius of gyration from that center in the Reply Log.  Tested with Chimera 1.11.2 on April 10th, 2017.
     21 * [attachment:radius-of-gyration-nomass.py radius-of-gyration-nomass.py].  Print center of mass and radius of gyration (not mass weighted) from that center in the Reply Log.  Tested with Chimera 1.11.2 on April 10th, 2017.
    1822 * [attachment:copymol.py copymol.py]. Copy a molecule and change atom coordinates. Tested with Chimera 1.11.2.  April 7, 2017.
    1923 * [attachment:volmin.py volmin.py]. Compute map minimum value without reading full map in memory. Tested with Chimera 1.11.  February 16, 2017.
    … …  
    2226 * [attachment:angles.py angles.py]. Measure angles between axes of two models in 2d planes. Tested with Chimera 1.11.  October 10, 2016.
    2327 * [attachment:triangles.py triangles.py]. Access surface vertices and triangles for density maps. Tested with Chimera 1.11.  September 7, 2016.
     28 * [attachment:getcolors.py getcolors.py].  Print out "modelcolor" commands equivalents for the current colors of open molecular models.  Tested with Chimera 1.11 on September 6, 2016.
    2429 * [attachment:syncregion.py syncregion.py]. Synchronize displayed regions of density maps. Tested with Chimera 1.11.  August 23, 2016.
    2530 * [attachment:surfval.py surfval.py]. Output text file of electrostatic values at surface points. Tested with Chimera 1.10.2.  July 5, 2016.
    … …  
    3136 * [attachment:surfinvert.py surfinvert.py]. Invert which part of surface is shown.  Used with hide dust to show only the dust for masking. Tested with Chimera 1.10.2.  December 8, 2015.
    3237 * [attachment:cube.py cube.py]. Extend density map to a cube. Tested with Chimera 1.10.2.  December 7, 2015.
     38 * [attachment:dipole.py dipole.py]. Print dipole moment to the reply log and show dipole vector of all open molecular models.  The models must already have charges assigned.  Tested with Chimera 1.10.2 on November 25th, 2015.
    3339 * [attachment:pp.py pp.py]. pipes and planks command. Tested with Chimera 1.10.2.  October 9, 2015.
    3440 * [attachment:helixtube.py helixtube.py]. htube command to show helices as tubes. Tested with Chimera 1.10.1.  August 12, 2015.
    … …  
    4046 * [attachment:atomdist.py atomdist.py]. Find minimum distance between two sets of atoms. Tested with Chimera 1.10.  November 17, 2014.
    4147 * [attachment:blend.py blend.py]. Blend 2 or more solid style maps. Tested with Chimera 1.9.  April 29, 2014.
     48 * [attachment:varbond.py varbond.py].  Show bond formation during a trajectory.  Usage described in [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-April/009759.html this chimera-users message].  Tested with Chimera 1.9 on April 7th, 2014.
    4249 * [attachment:insightgrid.py insightgrid.py]. Read Insight II grid file produced by rdock docking program. Tested with Chimera 1.9.  Feb 26, 2014.
    4350 * [attachment:changeaxes.py changeaxes.py]. Move atoms to use specified axes. Tested with Chimera 1.9.  Feb 25, 2014.
    … …  
    5865 * [attachment:eulermove.py eulermove.py]. Rotate a map by specified Euler angles. Tested with Chimera 1.7 daily build.  April 24, 2012.
    5966 * [attachment:vclip.py vclip.py]. Show the intersection and union of two maps. Tested with Chimera 1.7 daily build.  April 22, 2012.
     67 * [attachment:orient.py orient.py].  Rotate every open structure so that the major axis is parallel to the Y axis and the secondary axis is parallel to the X axis.  Tested with Chimera 1.7 on March 15th, 2012.
    6068 * [attachment:volumecenter.py volumecenter.py]. Place marker at center of mass of map. Tested with Chimera 1.6 daily build.  November 14, 2011.
    6169 * [attachment:marksurface.py marksurface.py]. Place markers at each vertex of selected surfaces. Tested with Chimera 1.6 daily build.  October 14, 2011.
     70 * [attachment:smoothMD.py smoothMD.py].  Rewrite a trajectory with averaged coordinates using nearby frames to produce smoother-looking motions.  Usage described in [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-April/002496.html this chimera-users message].  Tested with Chimera 1.6 on September 20th, 2011.
    6271 * [attachment:czone.py czone.py]. Color a surface to match nearby selected atoms. Tested with Chimera 1.6 daily build.  March 7, 2011.
    6372 * [attachment:readvol.py readvol.py]. Open volume data file, find size, xyz coordinates, data values. Tested with Chimera 1.6 daily build.  Feb 16, 2011.
    … …  
    7079 * [wiki:Scripts/MMTK Using Chimera with MMTK].  Tested with Chimera 1.5 daily build.  July 8, 2010.
    7180 * [attachment:edgesum.py edgesum.py]. Add values at edge of volume data.  Tested with Chimera 1.4.  June 21, 2010.
     81 * [attachment:torspace.py torspace.py]. Drive a torsion angle through 360 degrees and make a volume data set from the atom positions.  Tested with Chimera 1.5 on May 12th, 2010.  Could be improved by checking for clashes and by having occupancy vary based on VDW radius.  Written by Miguel Ortiz-Lombardia.
    7282 * [attachment:saveunitcell.py saveunitcell.py]. Save unit cell symmetry copies of a molecule.  Tested with Chimera 1.4.  April 26, 2010.
    7383 * [attachment:placeatom.py placeatom.py]. Place a new atom near an existing atom.  Tested with Chimera 1.4.  April 23, 2010.
    … …  
    94104 * [attachment:selLys.py selLys.py]. Select lysine NZ atoms within 8 angstroms of another lysine NZ and put distance monitors between them.  Difficult to do with normal selection language because of no way to exclude the base atoms of a zone selection from the zone test.  Tested with Chimera 1.4 daily build September 21, 2009 using PDB 1www.
    95105 * [attachment:disulphide.py disulphide.py]. Create disulphide bonds between unprotonated CYS SG atoms that are not already disulphide bonded and that meet reasonable bond-distance criteria.  Tested with Chimera 1.4 daily build November 11, 2009 using PDB 1gc1.
    96  * [attachment:dipole.py dipole.py]. Print dipole moment to the reply log and show dipole vector of all open molecular models.  The models must already have charges assigned.  Tested with Chimera 1.10.2 on November 25th, 2015.
    97  * [attachment:torspace.py torspace.py]. Drive a torsion angle through 360 degrees and make a volume data set from the atom positions.  Tested with Chimera 1.5 on May 12th, 2010.  Could be improved by checking for clashes and by having occupancy vary based on VDW radius.  Written by Miguel Ortiz-Lombardia.
    98  * [attachment:smoothMD.py smoothMD.py].  Rewrite a trajectory with averaged coordinates using nearby frames to produce smoother-looking motions.  Usage described in [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-April/002496.html this chimera-users message].  Tested with Chimera 1.6 on September 20th, 2011.
    99  * [attachment:radius-of-gyration-mass.py radius-of-gyration-mass.py].  Print center of mass and mass-weighted radius of gyration from that center in the Reply Log.  Tested with Chimera 1.11.2 on April 10th, 2017.
    100  * [attachment:radius-of-gyration-nomass.py radius-of-gyration-nomass.py].  Print center of mass and radius of gyration (not mass weighted) from that center in the Reply Log.  Tested with Chimera 1.11.2 on April 10th, 2017.
    101  * [attachment:orient.py orient.py].  Rotate every open structure so that the major axis is parallel to the Y axis and the secondary axis is parallel to the X axis.  Tested with Chimera 1.7 on March 15th, 2012.
    102  * [attachment:varbond.py varbond.py].  Show bond formation during a trajectory.  Usage described in [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-April/009759.html this chimera-users message].  Tested with Chimera 1.9 on April 7th, 2014.
    103  * [attachment:getcolors.py getcolors.py].  Print out "modelcolor" commands equivalents for the current colors of open molecular models.  Tested with Chimera 1.11 on September 6, 2016.
    104  * [attachment:worm.py worm.py].  Create a "worms" depiction based on mavConservation attribute.  Script easily edited to use different attribute and different worm widths.  Tested with Chimera 1.11.2 on July 13, 2017.
    105  * [attachment:pruneCoordSets.py pruneCoordSets.py].  Prune away inactive coordinate sets to reduce session-file size.  Tested with Chimera 1.13.1 on April 28, 2019
     106 
    106107
    107108= ChimeraX Python Scripts =